3TFJ

DMSP-dependent demethylase from P. ubique - with cofactor THF

3TFJ の概要

• エントリーDOI: 10.2210/pdb3tfj/pdb
• 関連するPDBエントリー: 3TFH 3TFI
• 分子名称: GcvT-like Aminomethyltransferase protein, (6S)-5,6,7,8-TETRAHYDROFOLATE, ACETATE ION, ... (6 entities in total)
• 機能のキーワード: demethylase, thf, transferase
• 由来する生物種: Candidatus Pelagibacter ubique
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 85012.55

構造登録者

Schuller, D.J.,Reisch, C.R.,Moran, M.A.,Whitman, W.B.,Lanzilotta, W.N. (登録日: 2011-08-15, 公開日: 2011-12-28, 最終更新日: 2023-09-13)

主引用文献

Schuller, D.J.,Reisch, C.R.,Moran, M.A.,Whitman, W.B.,Lanzilotta, W.N.
Structures of dimethylsulfoniopropionate-dependent demethylase from the marine organism Pelagabacter ubique.
Protein Sci., 21:289-298, 2012

PubMed Abstract: Dimethylsulfoniopropionate (DMSP) is a ubiquitous algal metabolite and common carbon and sulfur source for marine bacteria. DMSP is a precursor for the climatically active gas dimethylsulfide that is readily oxidized to sulfate, sulfur dioxide, methanesulfonic acid, and other products that act as cloud condensation nuclei. Although the environmental importance of DMSP metabolism has been known for some time, the enzyme responsible for DMSP demethylation by marine bacterioplankton, dimethylsufoniopropionate-dependent demethylase A (DmdA, EC 2.1.1.B5), has only recently been identified and biochemically characterized. In this work, we report the structure for the apoenzyme DmdA from Pelagibacter ubique (2.1 Å), as well as for DmdA co-crystals soaked with substrate DMSP (1.6 Å) or the cofactor tetrahydrofolate (THF) (1.6 Å). Surprisingly, the overall fold of the DmdA is not similar to other enzymes that typically utilize the reduced form of THF and in fact is a triple domain structure similar to what has been observed for the glycine cleavage T protein or sarcosine oxidase. Specifically, while the THF binding fold appears conserved, previous biochemical studies have shown that all enzymes with a similar fold produce 5,10-methylene-THF, while DmdA catalyzes a redox-neutral methyl transfer reaction to produce 5-methyl-THF. On the basis of the findings presented herein and the available biochemical data, we outline a mechanism for a redox-neutral methyl transfer reaction that is novel to this conserved THF binding domain.

PubMed: 22162093
DOI: 10.1002/pro.2015

実験手法

X-RAY DIFFRACTION (1.6 Å)